From what I gather, a professional cloner should copy only the data files, in order and in their current structure. They can read file delimiters (EOFs) so getting extra data should not be an issue... unless there are large gaps in the data. I would suggest running a defrag before cloning.
Most programs will attempt to copy the source in uncompressed format, but I imagine there are some which will copy it and compress it. You will need to be careful as many of these programs will require that you save the entire image to a location... eg, you will need ~100GB of free space somewhere, the image once saved can likely be split ony cds... though i'd suggest a dvd burner for fewer discs.
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